Хотите знать, если код ниже
if((input$app != "") && (input$variable != "") && (input$variable != "All") && (input$variable1 != "") && (input$variable1 != "All") && (input$variable2 != "") && (input$variable2 != "All"))
можно записать как
if((input$app != "") && (input$variable != c("","All")) && (input$variable1 != c("","All")) && (input$variable2 != c("","All")))